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Change .bai index for .csi index in samtools_index #391

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merged 5 commits into from
Aug 27, 2024
Merged

Change .bai index for .csi index in samtools_index #391

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86581c3
produce csi index instead of bai
atrigila Aug 26, 2024
d4cc98b
update tests to get csi
atrigila Aug 26, 2024
435f582
apply csi to all subworkflows using samtools_index
atrigila Aug 26, 2024
7d34115
update changelog
atrigila Aug 27, 2024
ff5ace9
Merge branch 'dev' into samtools_index_c
atrigila Aug 27, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#383]](https://github.com/nf-core/smrnaseq/pull/383) - Fix [parameter `--skip_fastp` throws an error](https://github.com/nf-core/smrnaseq/issues/263) - Fix parameter --skip_fastp.
- [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360) - Fix filter stats module and add filter contaminants test profile.
- [[#387]](https://github.com/nf-core/smrnaseq/pull/387) - Add nf-test to local module `blat_mirna` and fixes [contaminant filter failure because the Docker image for BLAT cannot be pulled](https://github.com/nf-core/smrnaseq/issues/354). Adds a small test profile to test contaminant filter results.
- [[#391]](https://github.com/nf-core/smrnaseq/pull/391) - Change `.bai` index for `.csi` index in `samtools_index` to fix [error because of large chromosomes](https://github.com/nf-core/smrnaseq/issues/132).

## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

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5 changes: 5 additions & 0 deletions conf/modules.config
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Expand Up @@ -314,6 +314,11 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'SAMTOOLS_INDEX' {
ext.args = '-c'
}

withName: 'NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
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48 changes: 24 additions & 24 deletions tests/test.nf.test
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Expand Up @@ -69,21 +69,21 @@ nextflow_pipeline {

{ assert snapshot(
path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"),
Expand All @@ -109,21 +109,21 @@ nextflow_pipeline {
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"),
Expand Down Expand Up @@ -233,21 +233,21 @@ nextflow_pipeline {

{ assert snapshot(
path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(),
path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(),
path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.csi").exists(),
path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"),
path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"),
path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"),
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32 changes: 16 additions & 16 deletions tests/test_index.nf.test
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Expand Up @@ -52,18 +52,18 @@ nextflow_pipeline {
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"),
path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"),
path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"),
Expand Down Expand Up @@ -95,15 +95,15 @@ nextflow_pipeline {
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"),
path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"),
path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"),
Expand Down
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